def mainchain():
#hide waters
cmd.hide("(solvent and (all))")
#hide cartoon
cmd.hide("cartoon")
cmd.hide("lines","not(name ca,c,n,o,h)")
#show mainchain sticks
cmd.show("sticks","((byres (all))&n;ca,c,n,o,h)")
util.color_chains("(all and elem c)",_self=cmd)
def chaincleanup():
cmd.hide("(solvent and (all))")
#cmd.hide("(all and hydro)")
cmd.show("cartoon" ,"all")
util.color_chains("(all and elem c)",_self=cmd)
cmd.show("sticks","((byres (all))&n;ca,c,n,o,h)")
cmd.hide("(all and hydro)")
#cmd.set('cartoon_transparency','0.25')
cmd.hide( 'sticks', 'elem H' )
cmd.hide( 'lines', 'elem H' )
def interface_analyser(name, dist_cuoff=10, animate=True):
'''
DESCRIPTION
displays the chains in different colors, showas cavity surfaces, and h.bonds with an interface cutoff
of 10 (default)
'''
# cmd.hide("lines")
cmd.select("interface", "none")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain" + letter
cmd.select(
chainname,
"%s and chain %s and not hetatm and not symbol w" % (name, letter))
if cmd.count_atoms("chain%s" % (letter)) > 0:
interfacename = "interface" + letter
cmd.select(
"not_this_chain",
"%s and not hetatm and not symbol w and not %s" %
(name, chainname))
cmd.select(
interfacename,
"%s and byres %s and (not_this_chain around %s)" %
(name, chainname, str(dist_cuoff)))
cmd.select("interface", "interface or %s" % (interfacename))
cmd.delete("not_this_chain")
cmd.delete("interface" + letter)
cmd.delete("chain%s" % (letter))
else:
cmd.delete(chainname)
cmd.hide("lines", name)
cmd.show("lines", "interface")
cmd.show("cartoon")
cmd.dist(
"%s_h.bonds" % name,
"interface",
"interface",
quiet=1,
mode=2,
label=0,
reset=1,
)
cmd.enable("%s_h.bonds" % name)
cmd.show("surface", "all")
cmd.set('surface_cavity_mode', 1)
util.color_chains("(all and elem c)", _self=cmd)
if animate:
cmd.zoom("interface", animate=-1)
cmd.orient("interface", animate=-1)
cmd.delete("interface")
cmd.remove("(all) and hydro")
def interface_analyser_with_surface(name='all',
chain_sur='A',
dist_cutoff=10,
animate=True):
cmd.select("interface", "none")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain" + letter
cmd.select(
chainname,
"%s and chain %s and not hetatm and not symbol w" % (name, letter))
if cmd.count_atoms("chain%s" % (letter)) > 0:
interfacename = "interface" + letter
cmd.select(
"not_this_chain",
"%s and not hetatm and not symbol w and not %s" %
(name, chainname))
cmd.select(
interfacename,
"%s and byres %s and (not_this_chain around %s)" %
(name, chainname, str(dist_cutoff)))
cmd.select("interface", "interface or %s" % (interfacename))
cmd.delete("not_this_chain")
cmd.delete("interface" + letter)
cmd.delete("chain%s" % (letter))
else:
cmd.delete(chainname)
cmd.hide("lines", name)
cmd.show("lines", "interface")
cmd.show("cartoon")
cmd.dist(
"%s_h.bonds" % name,
"interface",
"interface",
quiet=1,
mode=2,
label=0,
reset=1,
)
cmd.enable("%s_h.bonds" % name)
cmd.create("chain%s" % chain_sur,
name + " and chain %s" % chain_sur,
zoom=0)
cmd.show("surface", "chain%s" % chain_sur)
util.color_chains("(all and elem c)", _self=cmd)
if animate:
cmd.zoom("interface", animate=-1)
cmd.orient("interface", animate=-1)
cmd.delete("interface")
cmd.remove("(all) and hydro")
def color_by_chains():
for obj in cmd.get_names('objects'):
util.color_chains('%s and e. c' %obj)
def chain_cleanup():
cleanup()
util.color_chains("(all and elem c)",_self=cmd)